A functional polymorphism in the catechol-O-methyltransferase (COMT) gene (Val158Met) has been associated with a large number of human diseases and endophenotypes. The aim of this study was to develop a novel cost-effective assay to genotype this polymorphism. The novel assay was based on the combination of allele-specific PCR and high-resolution melting in a qPCR platform. Melt-curve analysis allowed a clear differentiation of the three genotypes. This novel assay could be implemented in the study of a large number of diseases and endophenotypes related to COMT dysfunction and could be extended for the analysis of other functional polymorphisms.